Genetic Variant DNAH7:c.4897-8dupT (chr2-195891811-G-GA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_018897.3(DNAH7):c.4897-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00028 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00027 ( 0 hom. )

Consequence

DNAH7
NM_018897.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.171

Variant links:

Genes affected

DNAH7 (HGNC:18661): (dynein axonemal heavy chain 7) DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]

DNAH7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS1

Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000268 (289/1076414) while in subpopulation AFR AF= 0.00367 (96/26182). AF 95% confidence interval is 0.00307. There are 0 homozygotes in gnomad4_exome. There are 142 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3 link	c.4897-8dupT		splice_region_variant, intron_variant	Intron 30 of 64	ENST00000312428.11	NP_061720.2	Q8WXX0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11 link	c.4897-8_4897-7insT		splice_region_variant, intron_variant	Intron 30 of 64	1	NM_018897.3	ENSP00000311273.6		Q8WXX0-1

Frequencies

GnomAD3 genomes

AF:

0.000287

AC:

AN:

149568

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000909

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000668

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000742

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000268

AC:

289

AN:

1076414

Hom.:

Cov.:

AF XY:

0.000266

AC XY:

142

AN XY:

534322

show subpopulations

Gnomad4 AFR exome

AF:

0.00367

Gnomad4 AMR exome

AF:

0.000281

Gnomad4 ASJ exome

AF:

0.000105

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000282

Gnomad4 FIN exome

AF:

0.0000699

Gnomad4 NFE exome

AF:

0.000185

Gnomad4 OTH exome

AF:

0.000268

GnomAD4 genome

AF:

0.000281

AC:

AN:

149678

Hom.:

Cov.:

AF XY:

0.000246

AC XY:

AN XY:

73038

show subpopulations

Gnomad4 AFR

AF:

0.000882

Gnomad4 AMR

AF:

0.0000667

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000742

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

2-195891811-GAAA-GAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over